9N6P | pdb_00009n6p

Room Temperature X-Ray Structure of SARS-CoV-2 Main Protease Mutant D48Y, P168 Deletion in Complex with Ensitrelvir

• PDB DOI: https://doi.org/10.2210/pdb9N6P/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-02-05 Released: 2025-07-30 
• Deposition Author(s): Bhandari, D., Kovalevsky, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.199 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir.

Bhandari, D., Gerlits, O., Keable, S., Coates, L., Aniana, A., Ghirlando, R., Nashed, N.T., Kovalevsky, A., Louis, J.M.

(2025) Commun Biol 8: 1061-1061

• PubMed: 40676153 
• DOI: https://doi.org/10.1038/s42003-025-08487-w
• Primary Citation Related Structures: 
  9N6J, 9N6L, 9N6M, 9N6N, 9N6P, 9N6R


• PubMed Abstract: 
  

  We investigate the effects of two naturally selected substitution and deletion (Δ) mutations, constituting part of the substrate binding subsites S2 and S4, on the structure, function, and inhibition of SARS CoV-2 main protease. Comparable to wild-type, MPro ^D48Y/ΔP168 undergoes N-terminal autoprocessing essential for stable dimer formation and mature-like catalytic activity. The structures are similar, but for an open active site conformation in MPro ^D48Y/ΔP168 and increased dynamics of the S2 helix, S5 loop, and the helical domain. Some dimer interface contacts exhibit shorter H bond distances corroborating the ~40-fold enhanced dimerization of the mutant although its thermal sensitivity to unfolding is 8 °C lower, relative to wild-type. ITC reveals a 3- and 5-fold decrease in binding affinity for nirmatrelvir and ensitrelvir, respectively, and similar GC373 affinity, to MPro ^D48Y/ΔP168 relative to wild-type. Structural differences in four inhibitor complexes of MPro ^D48Y/ΔP168 compared to wild-type are described. Consistent with enhanced dynamics, the S2 helix and S5 loop adopting a more open conformation appears to be a unique feature of MPro ^D48Y/ΔP168 both in the inhibitor-free and bound states. Our results suggest that mutational effects are compensated by changes in the conformational dynamics and thereby modulate N-terminal autoprocessing, K _dimer , catalytic efficiency, and inhibitor binding.

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Organizational Affiliation: 
• Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, USA.
Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. [e-mail].
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.33 kDa 
• Atom Count: 2,511 
• Modeled Residue Count: 301 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	305	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7YY (Subject of Investigation/LOI)	B [auth A]	6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione C22 H17 Cl F3 N9 O2 QMPBBNUOBOFBFS-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.199 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.26	α = 90
b = 83.331	β = 95.5
c = 91.004	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Bhandari, D., Kovalevsky, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release